Record store clerk Nick Brady begins to experience strange visions from an entity he calls VALIS that cause him to uproot his family and move to Los Angeles where he becomes a successful music company executive. Nick finds himself drawn into a dangerous political-mystical conspiracy of cosmic proportions.

Billy is a teenage outcast in search of his life's true meaning. Day by day, he slaves away at the local burger joint, only to return home to a paraplegic father, whose own dreams of happiness have faded away in an alcoholic haze. Nonetheless, Billy tries to bond with his delusional father, but cannot break through the many layers of pain and regret that surround him. Frustrated, Billy longs to escape the dead-end existence that has engulfed his father, and now appears to be closing in on him as well.

Crime writer Sean Flynn returns home to Riverport, North Carolina from New York after a long absence when authorities reopen the old murder case that ended his father's political career. To uncover the truth about a suspicious death and further his own literary ambitions, Sean must confront the shared demons that have long distanced him from his father, Chuck Flynn, a former District Attorney turned defense lawyer who is now trying the case and pissing his life away in a local bar across from the courthouse. As the trial unfolds, nothing about the case is what it first seemed, and it is the secret behind it coupled with the same forces that have kept them apart that will ultimately test father and son together in the end.